Also, I was wondering if you could answer another question for me. If I need to post this in another section, let me know.
When I tested the other ignition, m&w pro-10 and new distributor, I needed to set the timing again. But, when I lock in the timing through smanager at 16 degrees, the timing was way off. I had to advance the distributor until it maxed out. Once I got it set, it ran like crap as if it was too advanced even though the marks lined up on the pulley when locked to 16 degrees. Lots of poping, misfires, hesitation, would not rev ect. So I unlocked the timing, and let the engine warm up and adjusted the distributor until the marks lined up. That cleared up all the issues and I ended up running a PB in mph at 153. What could the issue be with the timing not setting right in the set timing window after removing the cpr kit. Any ideas, let me know. Thanks.

No, there is the tdc mark that is a single mark, then the 3 timing marks on the pulley with the center mark at 16 degrees. If I lock timing at 16 degrees I line it up with the center mark. If locked at 16 degrees and I set my gun to 16 degrees, then the tdc mark will line up. either way I did it, timing was off.

Yes it has, but not enough to take it out of adjustment range. Regardless, even when I get the timing set by locking it at 16 degrees and the timing light shows the center timing mark lined up correctly, the timing is way off, by like 12 degrees advanced. And in top of that when the CPR was on, timing wasn't out of adjustment range on the distributor.
I had to unlock it and set timing that way. Only then did it run right, no popping, hesitation or backfires. Revved appropriately and gave me a clean pass. 9.9@153mph. If I left the timing where the computer told me, I surely would have blown the motor.

Right, and when I do that, the single white line will line up. But the timing is still way off. You can tell by the way the engine is acting. It pops, hesitates, wont rev clean or even past 6k. When driving it, it jerks and backfires.
Could it just be in the timing tables? I mean it was originally tuned on the CPR, but does this with an m&w pro 1

I agree, but even with the same distributor that was working perfectly on the cpr kit, it did the exact same thing. Nothing mechanical changed.
Timing was set with the cpr
drove the car off the trailer and parked it
took the cpr off, left the dizzy on
put in the m&w pro - 10 to test
timing was way off and would not set
changed to a new dizzy, exactly the same

Its as if the timing window, even though its showing 16 degrees, it is actually doing 28 degrees BTDC.

close Smanager, reopen it, open your calibration that was saved on the hard drive and reupload to the ECU. If you use the set timing function make sure you properly close that window when you are done and don't' just unplug the USB or close the software. Beyond that there is nothing else besides a mechanical issue would cause this.